1. Open https://github.com/dlab-geo/r-geospatial-workshop
   • Download & unzip the zip file
   • Make a note of the folder in which it is located

2. Start RStudio and open a new script file

3. Install required libraries in RStudio - if you do not have them already

install.packages(
  c("sp","rgdal","tmap","classInt","RColorBrewer",
    "ggplot2","leaflet", "ggmap"), dependencies=TRUE
)

Intro to working with geospatial data in R

• Geospatial data files and formats
• Loading geospatial data in R
• R packages for working with geospatial data
• Coordinate reference systems & map projections
• Mapping geospatial data

Key goal is familiarity, competency takes lots of practice

Who are you?

Why are you here?

Open one of the tutorial files in a web browser

Slides r-geospatial-workshop-pt1.html

Tutorial r-geospatial-workshop-pt1-tutorial.html

Raw Code scripts/r-geospatial-workshop-pt1.R

Make sure you can cut and paste into RStudio # Geographic Data

are data about locations on or near the surface of the Earth.

represent location more specifically with coordinates

46.130479, -117.134167

Coordinates only make sense when associated with a CRS!

Geographic Coordinates: Latitude and Longitude

Define:

• the shape of the Earth

• the origin (0,0 point)

• the relationship between the system and the real world

• the units

Because of variations in these, there are many geographic CRSs!

The World Geodetic System of 1984 is the most widely used geographic coordinate reference system.

WGS84 is the default CRS for most GIS software

Almost all longitude and latitude data are assumed to be WGS84 unless otherwise specified

Historical data much trickier

You can

• dynamically determine spatial metrics like area, length, distance and direction

• spatial relationships like intersects, inside, contains, etc

and

• link data by location, like census data and crime data

Spatial data is a broader term than geographic data.

Methods for working with spatial data are valid for geospatial data

All spatial data are encoded with some type of coordinate reference system

Geospatial data require the CRS to be a model of locations on the Earth

Vector and Raster Data

Points, lines and Polygons

Regular grid of cells (or pixels)

• We won't be covering Raster data in this workshop*

software that can import, create, store, edit, visualize and analyze geospatial data

• represented as geometric data objects referenced to the surface of the earth via CRSs

• with methods to operate on those representations

We call software for working with geospatial data GIS

Geographic Information System

This term is commonly associated with desktop software applications.

Desktop GIS - ArcGIS, QGIS

Spatial Databases - PostgreSQL/PostGIS

Web-based GIS - ArcGIS Online, CARTO

Software geospatial data support - Tableau

Programming languages with geospatial data support

• R, Python, Javascript

You already use R

Reproducibility

Free & Open Source

Strong support for geospatial data and analysis

Cutting edge

Make sure you have the packages we are going to use installed and loaded

Make sure you have set your working directory to the location of the workshop files

install.packages(
  c("sp","rgdal","tmap","classInt","RColorBrewer",
    "ggplot2","leaflet", "ggmap"), dependencies=TRUE
)

There are many approaches to and packages for working with geospatial data in R.

One approach is to keep it simple and store geospatial data in a data frame.

This approach is most common when

• the data are point data in CSV files and

• you want to map rather than spatially transform or analyze the data

sf_properties_25ksample.csv

San Francisco Open Data Portal https://data.sfgov.org

SF Property Tax Rolls

This data set includes the Office of the Assessor-Recorder’s secured property tax roll spanning from 2007 to 2016.

We are using a subset of these data as a proxy for home values.

sfhomes <- read.csv('data/sf_properties_25ksample.csv', 
                    stringsAsFactors = FALSE)

# Take a look at first 5 rows and a few of the columns
sfhomes[1:5,c("YearBuilt","totvalue","AreaSquareFeet","Neighborhood",
              "NumBedrooms")]

Make sure your working directory is set to the folder where you downloaded the workshop files!

sfhomes <- read.csv('data/sf_properties_25ksample.csv', 
                    stringsAsFactors = FALSE)

# Take a look at first 5 rows and a few of the columns
sfhomes[1:5,c("YearBuilt","totvalue","AreaSquareFeet","Neighborhood",
              "NumBedrooms")]

##   YearBuilt totvalue AreaSquareFeet       Neighborhood NumBedrooms
## 1      1923  1031391           2250 West of Twin Peaks           0
## 2      1909   775300           5830   Presidio Heights           3
## 3      1915  1116772           1350     Inner Richmond           2
## 4      1947   860130           1162    Sunset/Parkside           0
## 5      1981   322749           1463     Outer Richmond           3

class(sfhomes)            # what is the data object type?
dim(sfhomes)              # how many rows and columns
str(sfhomes)              # display the structure of the object
head(sfhomes)             # take a look at the first 10 records
summary(sfhomes)          # explore the range of values
summary(sfhomes$totvalue) # explore the range of values for one column
hist(sfhomes$totvalue)    # histogram for the totvalue column

• What columns contain the geographic data?
• Are these data vector or raster data?
• What type of geometry do the data contain?
  • Points, lines, polygons, grid cells?
• What is the CRS of these data?

Use the R base plot function to create a simple map

plot(sfhomes$lon, sfhomes$lat) # using base plot function

Use the R base plot function to create a simple map

plot(sfhomes$lon, sfhomes$lat) # using base plot function

Most widely used plotting library in R

Not specifically for geospatial data

But can be used to make fabulous maps

Great choice if you already know ggplot2

Load the library

library(ggplot2)

Basic map with ggplot

library(ggplot2)

ggplot() + geom_point(data=sfhomes, aes(lon,lat))

Basic map with ggplot

ggplot() + geom_point(data=sfhomes, aes(lon,lat), size=1)

ggplot() + geom_point(data=sfhomes, aes(lon,lat), size=1) + coord_map()

Allows you to associate a map projection with geographic coord data.

Map Projection: mathematial transformation from curved to flat surface

A Projected CRS applies a map projection to a Geographic CRS

All introduce distortion,

• in shape, area, distance, direction, or combo

• the larger the area the greater the distortion

No one map projection best for all purposes

Selection depends on location, extent and purpose

Mercator is the default map projection used by the get_coord() function.

• You don't have to specify it!

It's important to know that you can customize the map projection and parameters if you wish.

But doing this is beyond the scope of this workshop.

Data driven symbology

ggplot() + geom_point(data=sfhomes, aes(lon,lat, col=totvalue)) + 
  coord_map()

What's happening here?

sfhomes_low2high <- sfhomes[order(sfhomes$totvalue, decreasing = FALSE),]

ggplot() + 
  geom_point(data=sfhomes_low2high, aes(lon,lat, col=totvalue)) + 
  coord_map()

Try it - Does the output map look different from previous one?

The order of the data in the data frame changes the map display!

Map the sfhomes data in decreasing order by totvalue.

sfhomes_high2low <- sfhomes[order(sfhomes$totvalue, decreasing = T),]
ggplot() + geom_point(data=sfhomes_high2low, aes(lon,lat, col=totvalue)) + 
  coord_map()

What does this code do?

sfhomes2010_15 <- subset(sfhomes_low2high, as.numeric(SalesYear) > 2009)

ggplot() +
  geom_point(aes(lon, lat, col=totvalue), data = sfhomes2010_15 )  +
  facet_wrap(~ SalesYear)

Visual spatial analysis!

Create basemaps on which you can display your data.

Use the Google Geocoding API to get coordinates for place names and addresses

and more…

Load the libary

library(ggmap)

Some ggmap functionality may require you to register a Google API key

Beginning July 2018 Google requires a credit card on file to access online APIs

So, we won't call Google APIs in this tutorial.

This set up is beyound the scope of this workshop but we want you to know its there if you want to use the Google Geocoder which is excellent.

If you have problems with ggmap you may need to reinstall the library from github.

• See this StackOverflow discussion

Alternatively, just follow along without trying while we demo!

#devtools::install_github("dkahle/ggmap")
#library(ggmap)

ggmap uses the get_map function to fetch map tiles to display in your map.

get_map uses a number of online mapping services including Google, Stamen and OpenStreetMap (OSM)

get_map requires as input a location, expressed as point coordinates.

See ?get_map for details

Let's fetch a simple map on which we can display our points

Here we are centering the map on San Francisco & using the stamen toner-lite basemap.

sf_center_point <- c(lon=-122.445144, lat=37.769335 )
sf_map <- get_map(sf_center_point, source="stamen", maptype="toner-lite")  

## Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=37.769335,-122.445144&zoom=10&size=640x640&scale=2&maptype=terrain&sensor=false

## Map from URL : http://tile.stamen.com/toner-lite/10/162/394.png

## Map from URL : http://tile.stamen.com/toner-lite/10/163/394.png

## Map from URL : http://tile.stamen.com/toner-lite/10/164/394.png

## Map from URL : http://tile.stamen.com/toner-lite/10/162/395.png

## Map from URL : http://tile.stamen.com/toner-lite/10/163/395.png

## Map from URL : http://tile.stamen.com/toner-lite/10/164/395.png

## Map from URL : http://tile.stamen.com/toner-lite/10/162/396.png

## Map from URL : http://tile.stamen.com/toner-lite/10/163/396.png

## Map from URL : http://tile.stamen.com/toner-lite/10/164/396.png

## Map from URL : http://tile.stamen.com/toner-lite/10/162/397.png

## Map from URL : http://tile.stamen.com/toner-lite/10/163/397.png

## Map from URL : http://tile.stamen.com/toner-lite/10/164/397.png

ggmap(sf_map)

Syntax similar to ggplot

But ggmap takes the name of the map object returned by get_map()

# ggplot() +

ggmap(sf_map) + 
  geom_point(data=sfhomes, aes(x=lon, y=lat, col=totvalue))

ggmap(sf_map) +
  geom_point(data=sfhomes, aes(x=lon, y=lat, col=totvalue))

That map is fine but the zoom level isn't right.

We want to zoom in on the data by setting the map extent.

We can set the map extent by centering the map on our data and increasing the zoom level.

• Note: get_map prints a lot of messages to the screen!

# Get the center point of the data
sf_ctr <- c(lon = mean(sfhomes$lon), lat = mean(sfhomes$lat))
sf_ctr  # take a look
 
# create the map - setting the zoom level to 12
sf_basemap <- get_map(sf_ctr, source="stamen", maptype="toner-lite", zoom=12)

## Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=37.758403,-122.439444&zoom=12&size=640x640&scale=2&maptype=terrain&sensor=false

## Map from URL : http://tile.stamen.com/toner-lite/12/653/1582.png

## Map from URL : http://tile.stamen.com/toner-lite/12/654/1582.png

## Map from URL : http://tile.stamen.com/toner-lite/12/655/1582.png

## Map from URL : http://tile.stamen.com/toner-lite/12/656/1582.png

## Map from URL : http://tile.stamen.com/toner-lite/12/653/1583.png

## Map from URL : http://tile.stamen.com/toner-lite/12/654/1583.png

## Map from URL : http://tile.stamen.com/toner-lite/12/655/1583.png

## Map from URL : http://tile.stamen.com/toner-lite/12/656/1583.png

## Map from URL : http://tile.stamen.com/toner-lite/12/653/1584.png

## Map from URL : http://tile.stamen.com/toner-lite/12/654/1584.png

## Map from URL : http://tile.stamen.com/toner-lite/12/655/1584.png

## Map from URL : http://tile.stamen.com/toner-lite/12/656/1584.png

Now, view the data on top of the sf_basemap with ggmap

ggmap(sf_basemap) +
   geom_point(data=sfhomes, aes(x=lon, y=lat, col=totvalue))

Create a ggmap that uses the customized sf_basemap

• overlay the sfhomes data for `2015

• color code the points by totvalue

# FIRST - subset the data
sfhomes15 <- subset(sfhomes, as.numeric(SalesYear) == 2015)
#
sfhomes15_map <- ggmap(sf_basemap) +
  geom_point(data=sfhomes15, aes(x=lon, y=lat, col=totvalue))

Display the results

sfhomes15_map

Finally, let's add another geospatial data layer to our ggmap.

You can use this method to add as many layers as you want to a ggmap or ggplot.

Use the read.csv function to read in a file of Bart Station locations. What is the name of the column with the longitude values? latitude?

bart <- read.csv("./data/bart.csv")

# take a look
head (bart)

##           X        Y             STATION OPERATOR DIST  CO
## 1 -122.2833 37.87406      NORTH BERKELEY     BART    4 ALA
## 2 -122.2682 37.86969   DOWNTOWN BERKELEY     BART    4 ALA
## 3 -122.2701 37.85321               ASHBY     BART    4 ALA
## 4 -122.2518 37.84451           ROCKRIDGE     BART    4 ALA
## 5 -122.2671 37.82871           MACARTHUR     BART    4 ALA
## 6 -122.2684 37.80808 19TH STREET/OAKLAND     BART    4 ALA

sfmap_with_bart <- ggmap(sf_basemap) +
  geom_point(data=sfhomes15, aes(x=lon, y=lat))  +
  geom_point(data=bart, aes(x=X,y=Y), col="red", size=3) 

sfmap_with_bart

## Warning: Removed 34 rows containing missing values (geom_point).

SF Landmarks

data/landmarks.csv

landmarks <- read.csv("./data/landmarks.csv")
head(landmarks)

##           X       Y id             name
## 1 -13626151 4551548  1       Coit Tower
## 2 -13630804 4544523  2       Twin Peaks
## 3 -13627654 4548289  3        City Hall
## 4 -13635101 4546904  4 Golden Gate Park

Create a map of the SF homes, BART Stations and Landmarks on top of the basemap.

sfmap_bart_landmarks <- ggmap(sf_basemap) +
  geom_point(data=sfhomes15, aes(x=lon, y=lat))  +
  geom_point(data=bart, aes(x=X,y=Y), col="red", size=3) +
  geom_point(data=landmarks, aes(x=X,y=Y), shape=22, 
             col="black", fill="grey", size=4)

All good - are all layers displayed? If not, why not?

## Warning: Removed 34 rows containing missing values (geom_point).

## Warning: Removed 4 rows containing missing values (geom_point).

There are limits to what you can do with geospatial data stored in a data frame.

The Landmark data do not have geographic coordinates - longitude and latitude.

You can't map these with ggmap.

##           X       Y id             name
## 1 -13626151 4551548  1       Coit Tower
## 2 -13630804 4544523  2       Twin Peaks
## 3 -13627654 4548289  3        City Hall
## 4 -13635101 4546904  4 Golden Gate Park

The ESRI Shapefile is the most common file format for geospatial data.

ggplot and ggmap cannot directly read in or plot shapefile data.

• though you can do it with a round-about set of commands :(

ggplot & ggmap can't answer questions like

• What properties are in the Noe Valley neighborhood?

• What is the average property value in each SF neighborhood?

• What is the area of each SF Neighborhood and the property density?

• What properties are within walking distance (.25 miles) of the Mission neighborhood?

You need spatial data objects and spatial methods for that!

Classes and Methods for Spatial Data

The SP package is most commonly used to construct and manipulate spatial data objects in R.

Hundreds of other R packages that do things with spatial data typically build on SP objects.

library(sp)

Take a look at the different types of spatial object classes supported by sp

getClass("Spatial") 

## Class "Spatial" [package "sp"]
## 
## Slots:
##                               
## Name:         bbox proj4string
## Class:      matrix         CRS
## 
## Known Subclasses: 
## Class "SpatialPoints", directly
## Class "SpatialMultiPoints", directly
## Class "SpatialGrid", directly
## Class "SpatialLines", directly
## Class "SpatialPolygons", directly
## Class "SpatialPointsDataFrame", by class "SpatialPoints", distance 2
## Class "SpatialPixels", by class "SpatialPoints", distance 2
## Class "SpatialMultiPointsDataFrame", by class "SpatialMultiPoints", distance 2
## Class "SpatialGridDataFrame", by class "SpatialGrid", distance 2
## Class "SpatialLinesDataFrame", by class "SpatialLines", distance 2
## Class "SpatialPixelsDataFrame", by class "SpatialPoints", distance 3
## Class "SpatialPolygonsDataFrame", by class "SpatialPolygons", distance 2

We use the S*DF objects most frequently!

• SpatialPointsDataFrame, SpatialLinesDataFrame, SpatialPolygonsDataFrame

Let's transform the sfhomes15 data frame to an sp object of type SpatialPointsDataFrame

Use the sp::coordinates() method

• Sets or retrieves spatial coordinates

When transforming a DF to SPDF you are setting the coordinates.

Note - the transformation happens in place!

sfhomes15_sp <- sfhomes15  # Make a copy - why?

class(sfhomes15_sp)  # check the class of the object

coordinates(sfhomes15_sp) <- c('lon','lat')  #  Make it spatial
                                             #  ORDER MATTERS!!

class(sfhomes15_sp)  # check the class of the object

sfhomes15_sp <- sfhomes15  # Make a copy - why?

class(sfhomes15_sp)  # check the class of the object

## [1] "data.frame"

coordinates(sfhomes15_sp) <- c('lon','lat')  #  Make it spatial - ORDER MATTERS!!

class(sfhomes15_sp)  # check the class of the object

## [1] "SpatialPointsDataFrame"
## attr(,"package")
## [1] "sp"

You transformed a data frame to an SPDF using:

coordinates(sfhomes15_sp) <- c('lon','lat')

Now try this:

coordinates(sfhomes15_sp)

coordinates(sfhomes15_sp)

##             lon      lat
## 24    -122.4741 37.73601
## 35    -122.3965 37.75920
## 76    -122.3942 37.77181
## 79    -122.4754 37.71518
## 85    -122.4210 37.75876
## 90    -122.4149 37.79362
## 92    -122.4370 37.74020
## 98    -122.4437 37.78881
## 223   -122.4754 37.71492
## 229   -122.3919 37.78868
## 273   -122.3968 37.77945
## 341   -122.5040 37.75515
## 363   -122.4041 37.76422
## 366   -122.3934 37.77764
## 388   -122.4166 37.74931
## 451   -122.4112 37.73683
## 467   -122.4507 37.76448
## 473   -122.3990 37.75450
## 487   -122.4195 37.76649
## 534   -122.4225 37.78676
## 548   -122.4410 37.70854
## 549   -122.5009 37.74485
## 550   -122.4220 37.73048
## 559   -122.4947 37.75832
## 567   -122.3942 37.77181
## 595   -122.4187 37.80469
## 624   -122.4019 37.77323
## 631   -122.4229 37.80586
## 646   -122.4225 37.78676
## 658   -122.3919 37.78868
## 665   -122.4261 37.74349
## 668   -122.3904 37.78139
## 683   -122.4458 37.74398
## 774   -122.3883 37.73754
## 776   -122.4767 37.75347
## 864   -122.4326 37.74229
## 974   -122.4380 37.72624
## 1018  -122.4452 37.76906
## 1097  -122.4937 37.77999
## 1155  -122.5047 37.75390
## 1164  -122.4498 37.75451
## 1167  -122.4055 37.80424
## 1188  -122.4194 37.75596
## 1242  -122.4088 37.77953
## 1273  -122.4331 37.76019
## 1374  -122.3918 37.77899
## 1379  -122.4070 37.75674
## 1487  -122.4236 37.77800
## 1598  -122.4758 37.75497
## 1600  -122.4419 37.74582
## 1618  -122.5030 37.74587
## 1668  -122.3989 37.78990
## 1698  -122.4236 37.77800
## 1747  -122.3972 37.76314
## 1755  -122.4434 37.75159
## 1768  -122.4242 37.80551
## 1804  -122.4549 37.76402
## 1828  -122.4320 37.78195
## 1833  -122.4405 37.71825
## 1913  -122.4146 37.74714
## 1999  -122.3942 37.77181
## 2024  -122.4676 37.71048
## 2033  -122.4249 37.76548
## 2066  -122.4243 37.75206
## 2073  -122.4097 37.77613
## 2096  -122.3996 37.73859
## 2248  -122.4045 37.79929
## 2258  -122.4442 37.78322
## 2285  -122.3919 37.78868
## 2314  -122.4026 37.77879
## 2329  -122.4368 37.78228
## 2339  -122.4240 37.74366
## 2355  -122.4126 37.79035
## 2416  -122.4579 37.72632
## 2428  -122.4089 37.79286
## 2436  -122.4409 37.80451
## 2443  -122.4127 37.78995
## 2500  -122.4357 37.76468
## 2508  -122.4666 37.76347
## 2537  -122.4870 37.74605
## 2538  -122.3942 37.77181
## 2627  -122.4219 37.77389
## 2692  -122.3958 37.77705
## 2717  -122.4116 37.77806
## 2734  -122.4290 37.72977
## 2793  -122.4764 37.73390
## 2914  -122.4183 37.76712
## 2969  -122.4711 37.72241
## 2975  -122.4393 37.78018
## 3127  -122.4393 37.78951
## 3157  -122.3702 37.72838
## 3205  -122.4398 37.78746
## 3262  -122.4540 37.78251
## 3288  -122.4698 37.75298
## 3296  -122.4607 37.73104
## 3306  -122.4081 37.77962
## 3354  -122.4849 37.74663
## 3403  -122.4209 37.75792
## 3436  -122.4854 37.74788
## 3471  -122.4856 37.78116
## 3485  -122.4177 37.80345
## 3516  -122.4354 37.72201
## 3578  -122.4199 37.77606
## 3611  -122.4269 37.80229
## 3658  -122.4108 37.76534
## 3754  -122.3888 37.72872
## 3772  -122.3891 37.73264
## 4023  -122.4827 37.77762
## 4025  -122.4450 37.76430
## 4058  -122.4328 37.71546
## 4076  -122.4660 37.74828
## 4111  -122.5023 37.74333
## 4114  -122.4970 37.74468
## 4140  -122.4741 37.73601
## 4150  -122.4060 37.79853
## 4249  -122.4302 37.74726
## 4270  -122.4194 37.76710
## 4287  -122.4676 37.71048
## 4369  -122.4950 37.73327
## 4376  -122.3919 37.78868
## 4393  -122.3972 37.77570
## 4427  -122.4332 37.77869
## 4466  -122.4786 37.77394
## 4469  -122.4210 37.76470
## 4483  -122.4318 37.71761
## 4514  -122.4214 37.78139
## 4526  -122.4153 37.74047
## 4527  -122.4209 37.79368
## 4555  -122.4145 37.79167
## 4561  -122.3910 37.78938
## 4566  -122.4031 37.79058
## 4578  -122.3906 37.75501
## 4579  -122.4154 37.74537
## 4592  -122.3922 37.78607
## 4599  -122.4385 37.75980
## 4602  -122.4785 37.76295
## 4618  -122.4137 37.79099
## 4648  -122.4635 37.76461
## 4663  -122.4160 37.74563
## 4669  -122.3918 37.77899
## 4759  -122.4911 37.75318
## 4800  -122.4137 37.79099
## 4825  -122.4147 37.72528
## 4853  -122.4388 37.75978
## 4864  -122.3696 37.72900
## 4896  -122.4245 37.79493
## 4899  -122.3902 37.75236
## 4921  -122.5103 37.77369
## 4939  -122.3930 37.73299
## 4944  -122.3919 37.78868
## 4970  -122.4646 37.77383
## 4986  -122.3904 37.78139
## 5053  -122.4287 37.77484
## 5085  -122.4244 37.78587
## 5104  -122.4255 37.72744
## 5108  -122.4364 37.77781
## 5109  -122.4394 37.80326
## 5114  -122.4853 37.75287
## 5188  -122.4302 37.74806
## 5228  -122.3881 37.73174
## 5247  -122.4242 37.80551
## 5252  -122.4296 37.79988
## 5261  -122.4048 37.79879
## 5287  -122.4335 37.79946
## 5288  -122.4611 37.73481
## 5316  -122.3918 37.77899
## 5320  -122.4481 37.77945
## 5321  -122.4477 37.71766
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## 22007 -122.4195 37.74526
## 22024 -122.5006 37.75075
## 22064 -122.4569 37.75564
## 22085 -122.4497 37.72884
## 22111 -122.3933 37.77891
## 22167 -122.5041 37.73937
## 22254 -122.3992 37.79825
## 22255 -122.4107 37.77166
## 22273 -122.4448 37.71416
## 22324 -122.3986 37.71395
## 22340 -122.4376 37.75052
## 22499 -122.4438 37.72965
## 22531 -122.4141 37.77608
## 22533 -122.4409 37.74887
## 22549 -122.4431 37.71275
## 22554 -122.4009 37.76461
## 22600 -122.4362 37.74701
## 22607 -122.4753 37.71516
## 22673 -122.4131 37.74787
## 22739 -122.3919 37.78868
## 22801 -122.4709 37.75504
## 22802 -122.4014 37.77974
## 22820 -122.4887 37.77819
## 22870 -122.4367 37.76372
## 22871 -122.4507 37.72158
## 22896 -122.4342 37.74955
## 22924 -122.4460 37.71426
## 22931 -122.4210 37.74497
## 22951 -122.4948 37.77410
## 23000 -122.4254 37.76334
## 23036 -122.4163 37.80401
## 23045 -122.3996 37.77438
## 23056 -122.4753 37.71487
## 23074 -122.3696 37.72900
## 23117 -122.4223 37.79267
## 23135 -122.3942 37.77181
## 23154 -122.4648 37.75510
## 23172 -122.4415 37.78044
## 23173 -122.4835 37.78257
## 23251 -122.4119 37.71432
## 23267 -122.4263 37.71022
## 23308 -122.4769 37.76468
## 23356 -122.4613 37.71719
## 23400 -122.4689 37.77570
## 23433 -122.4753 37.71553
## 23467 -122.3928 37.78205
## 23478 -122.4855 37.75523
## 23486 -122.4276 37.72233
## 23503 -122.4108 37.76534
## 23519 -122.4454 37.76390
## 23535 -122.4639 37.76393
## 23540 -122.4599 37.72230
## 23542 -122.4860 37.78680
## 23598 -122.3910 37.78938
## 23601 -122.3922 37.78607
## 23721 -122.4452 37.71600
## 23782 -122.4012 37.75378
## 23790 -122.5038 37.75594
## 23828 -122.3957 37.73636
## 23881 -122.3906 37.75501
## 23895 -122.4517 37.72883
## 23896 -122.4011 37.77047
## 23913 -122.4734 37.75749
## 23918 -122.4676 37.71048
## 23919 -122.4936 37.77938
## 23991 -122.4418 37.73477
## 24130 -122.4544 37.76267
## 24185 -122.4891 37.77817
## 24223 -122.4194 37.75596
## 24282 -122.4934 37.73923
## 24314 -122.4577 37.74434
## 24326 -122.3880 37.73296
## 24374 -122.3696 37.72900
## 24393 -122.4372 37.75934
## 24401 -122.4517 37.73329
## 24402 -122.4711 37.74663
## 24504 -122.4536 37.70915
## 24546 -122.4544 37.78545
## 24554 -122.4395 37.75941
## 24574 -122.3997 37.75216
## 24607 -122.4836 37.77285
## 24639 -122.4824 37.75738
## 24659 -122.3920 37.72865
## 24674 -122.4760 37.78306
## 24700 -122.4138 37.73519
## 24716 -122.4922 37.77477
## 24724 -122.4374 37.75893
## 24742 -122.4704 37.78430
## 24781 -122.4137 37.79099
## 24794 -122.4016 37.75125
## 24816 -122.4009 37.72799
## 24840 -122.4704 37.74936
## 24872 -122.4236 37.77800
## 24896 -122.4441 37.73437
## 24922 -122.4446 37.77193
## 24940 -122.4192 37.72509
## 24949 -122.4356 37.72596
## 24966 -122.3919 37.78868
## 24983 -122.4458 37.73512
## 24986 -122.4668 37.77558

str(sfhomes15) # the data frame

str(sfhomes15_sp) # the data frame

str(sfhomes15) # the data frame

## 'data.frame':    835 obs. of  19 variables:
##  $ FiscalYear      : int  2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
##  $ SalesDate       : chr  "2015-08-21" "2015-08-13" "2015-12-29" "2015-08-26" ...
##  $ Address         : chr  "0000 2760 19TH                AV0015" "0000 0560AMISSOURI            ST0000" "0000 0718 LONG BRIDGE         ST1202" "0000 0103 SUMMIT              WY0000" ...
##  $ YearBuilt       : int  1979 2003 2016 NA 2015 1961 1973 1900 NA 2015 ...
##  $ NumBedrooms     : int  2 2 2 3 3 3 3 2 0 2 ...
##  $ NumBathrooms    : int  2 2 2 3 3 3 3 2 0 2 ...
##  $ NumRooms        : int  5 5 5 6 7 7 7 5 0 0 ...
##  $ NumStories      : int  0 1 1 0 1 14 2 1 0 1 ...
##  $ NumUnits        : int  1 1 1 1 1 1 1 1 0 1 ...
##  $ AreaSquareFeet  : int  1595 1191 1346 2133 1266 1840 2075 1256 0 1520 ...
##  $ ImprovementValue: int  432500 701280 1512093 582108 850000 1154846 484544 810169 486872 962500 ...
##  $ LandValue       : int  432500 701280 748900 873161 850000 1154846 1130604 1890395 1136036 962500 ...
##  $ Neighborhood    : chr  "West of Twin Peaks" "Potrero Hill" "Mission Bay" "Lakeshore" ...
##  $ Location        : chr  "(37.7360097396496, -122.474067310226)" "(37.759197817252, -122.396516184449)" "(37.7718055392903, -122.394186974738)" "(37.7151803909173, -122.475425717555)" ...
##  $ SupeDistrict    : int  7 10 6 7 9 3 8 2 7 6 ...
##  $ totvalue        : int  865000 1402560 2260993 1455269 1700000 2309692 1615148 2700564 1622908 1925000 ...
##  $ SalesYear       : int  2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
##  $ lat             : num  37.7 37.8 37.8 37.7 37.8 ...
##  $ lon             : num  -122 -122 -122 -122 -122 ...

str(sfhomes15_sp) # the SPDF

## Formal class 'SpatialPointsDataFrame' [package "sp"] with 5 slots
##   ..@ data       :'data.frame':  835 obs. of  17 variables:
##   .. ..$ FiscalYear      : int [1:835] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
##   .. ..$ SalesDate       : chr [1:835] "2015-08-21" "2015-08-13" "2015-12-29" "2015-08-26" ...
##   .. ..$ Address         : chr [1:835] "0000 2760 19TH                AV0015" "0000 0560AMISSOURI            ST0000" "0000 0718 LONG BRIDGE         ST1202" "0000 0103 SUMMIT              WY0000" ...
##   .. ..$ YearBuilt       : int [1:835] 1979 2003 2016 NA 2015 1961 1973 1900 NA 2015 ...
##   .. ..$ NumBedrooms     : int [1:835] 2 2 2 3 3 3 3 2 0 2 ...
##   .. ..$ NumBathrooms    : int [1:835] 2 2 2 3 3 3 3 2 0 2 ...
##   .. ..$ NumRooms        : int [1:835] 5 5 5 6 7 7 7 5 0 0 ...
##   .. ..$ NumStories      : int [1:835] 0 1 1 0 1 14 2 1 0 1 ...
##   .. ..$ NumUnits        : int [1:835] 1 1 1 1 1 1 1 1 0 1 ...
##   .. ..$ AreaSquareFeet  : int [1:835] 1595 1191 1346 2133 1266 1840 2075 1256 0 1520 ...
##   .. ..$ ImprovementValue: int [1:835] 432500 701280 1512093 582108 850000 1154846 484544 810169 486872 962500 ...
##   .. ..$ LandValue       : int [1:835] 432500 701280 748900 873161 850000 1154846 1130604 1890395 1136036 962500 ...
##   .. ..$ Neighborhood    : chr [1:835] "West of Twin Peaks" "Potrero Hill" "Mission Bay" "Lakeshore" ...
##   .. ..$ Location        : chr [1:835] "(37.7360097396496, -122.474067310226)" "(37.759197817252, -122.396516184449)" "(37.7718055392903, -122.394186974738)" "(37.7151803909173, -122.475425717555)" ...
##   .. ..$ SupeDistrict    : int [1:835] 7 10 6 7 9 3 8 2 7 6 ...
##   .. ..$ totvalue        : int [1:835] 865000 1402560 2260993 1455269 1700000 2309692 1615148 2700564 1622908 1925000 ...
##   .. ..$ SalesYear       : int [1:835] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
##   ..@ coords.nrs : int [1:2] 19 18
##   ..@ coords     : num [1:835, 1:2] -122 -122 -122 -122 -122 ...
##   .. ..- attr(*, "dimnames")=List of 2
##   .. .. ..$ : chr [1:835] "24" "35" "76" "79" ...
##   .. .. ..$ : chr [1:2] "lon" "lat"
##   ..@ bbox       : num [1:2, 1:2] -122.5 37.7 -122.4 37.8
##   .. ..- attr(*, "dimnames")=List of 2
##   .. .. ..$ : chr [1:2] "lon" "lat"
##   .. .. ..$ : chr [1:2] "min" "max"
##   ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
##   .. .. ..@ projargs: chr NA

You can see from str(sfhomes) that a SPDF object is a collection of slots or components. The key ones are:

• @data data frame of attributes that describe each location
• @coords the coordinates for each geometric object - here points
• @bbox the min and max bounding coordinates
• @proj4string the coordinate reference system defintion as a string

Explore the object in the Environment window

Review the output of each of these:

summary(sfhomes15_sp)
head(sfhomes15_sp@data)
class(sfhomes15_sp@data)

sfhomes15_sp@bbox
bbox(sfhomes15_sp)

head(sfhomes15_sp@coords)
head(sfhomes15_sp$lat)
head(sfhomes15_sp$lon)

sfhomes15_sp@proj4string
proj4string(sfhomes15_sp)

Look at sfhomes15_sp in the environment window

Are all the columns that were present in sfhomes15 also in sfhomes15_sp?

Is there a slot in sfhomes15_sp without data?

proj4string(sfhomes15_sp) # get a CRS object

## [1] NA

plot(sfhomes15_sp)  # using sp::plot

We created great maps of sfhomes point data with ggplot and ggmap.

Then we created a simple map of the SPDF with plot.

We aren't seeing the value of sp objects just yet.

rgdal is an R port of the powerful and widely used GDAL library.

It is the most commonly used R library for importing and exporting spatial data.

• OGR: for vector data: readOGR() and writeOGR()

• GDAL for raster data: readGDAL() and writeGDAL()

library(rgdal)

## rgdal: version: 1.2-8, (SVN revision 663)
##  Geospatial Data Abstraction Library extensions to R successfully loaded
##  Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
##  Path to GDAL shared files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/gdal
##  Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
##  Path to PROJ.4 shared files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/proj
##  Linking to sp version: 1.2-4

# See what file types are supported by rgdal drivers
# ogrDrivers()$name

gdal.org

?readOGR

For more info on working with rgdal to load different types of spatial data in R see this excellent tutorial by Zev Ross.

Take a look at the file(s)

dir("data", pattern="sf_boundary")

## [1] "sf_boundary.dbf" "sf_boundary.prj" "sf_boundary.shp" "sf_boundary.shx"

sfboundary <- readOGR(dsn="data",layer="sf_boundary")

## OGR data source with driver: ESRI Shapefile 
## Source: "data", layer: "sf_boundary"
## with 1 features
## It has 3 fields

# or
# sfboundary <- readOGR("data","sf_boundary")
# but not
#sfboundary <- readOGR(dsn="data/",layer="sf_boundary")

What type of sp object is sfboundary? How many features are in the object?

class(sfboundary)
str(sfboundary) 
head(sfboundary@data)  

Explore the object in the Envi window

How?

plot(sfboundary)

plot(sfboundary)
points(sfhomes15_sp, col="red")

Where are the points? What's wrong?

plot(sfboundary)
points(sfhomes15_sp, col="red")

Compare the CRSs, are they the same?

proj4string(sfboundary)
proj4string(sfhomes15_sp)

proj4string(sfboundary)

## [1] "+proj=utm +zone=10 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"

proj4string(sfhomes15_sp)

## [1] NA

sfboundary@bbox

##         min       max
## x  542696.6  556659.9
## y 4173563.7 4185088.6

sfhomes15_sp@bbox

##            min        max
## lon -122.51072 -122.36964
## lat   37.70854   37.80612

The #1 reason…

All sp objects should have a defined CRS

If not, one needs to be assigned to the object

• This is called defining a projection

• This doesn't change the coordinates

All sp objects should have the same CRS.

This CRS should be defined in the proj4string slot.

• When they don't, they need to be transformed to a common CRS.

• This is called a projection transformation,
  • or projecting or reprojection.

Projection transformation returns a new spatial object with the transformed coordinates

GIS software - or software for working with geospatial data - will have a database of definitions for thousands of Earth referenced coordinate systems

and methods for using those CRS definitions to define or transform a CRS.

So, do we need to define the CRS of either

• sfboundary or

• sfhomes15_sp?

If yes, which one? How can you tell?

We need to know

• what the data's CRS is
• how to define it for the sp object

bbox(sfhomes15_sp)

##            min        max
## lon -122.51072 -122.36964
## lat   37.70854   37.80612

Use the sp function CRS() to create a CRS object

Then, use the sp::proj4string() to assign it

# Define the CRS for sfhomes15_sp as WGS84

proj4string(sfhomes15_sp) <- CRS("+proj=longlat 
                               +ellps=WGS84 +datum=WGS84 +no_defs")  

The WGS84 proj4 string

CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")

The WGS84 epsg code

CRS("+init=epsg:4326")

EPSG refers to the group that defined these

• European Petroleum Survey Group

EPSG codes are more commonly used. Can you guess why?

# use an EPSG code for WGS84
proj4string(sfhomes15_sp) <- CRS("+init=epsg:4326") 

# or enter the parameter string
# proj4string(sfhomes15_sp) <- CRS("+proj=longlat 
#                               +ellps=WGS84 +datum=WGS84 +no_defs")  

Proj4 is the standard library for defining and transforming map projections and coordinate reference systems.

Here is an example file of proj4 CRS definitions

Once you set the CRS you can check it with the same function.

proj4string(sfhomes15_sp)

## [1] "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0"

proj4string() can get or set the CRS

CRS() is used to define the CRS of an sp object

The following are equivalent

# Define the CRS with the parameter string
proj4string(sfhomes15_sp) <- CRS("+proj=longlat 
                              +ellps=WGS84 +datum=WGS84 +no_defs")  

# Define the CRS with an EPSG code for WGS84
proj4string(sfhomes15_sp) <- CRS("+init=epsg:4326") 

epsg codes are used as short-hand for CRSs definitions

Are they both defined? Are they the same?

proj4string(sfboundary)

## [1] "+proj=utm +zone=10 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"

proj4string(sfhomes15_sp)

## [1] "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0"

proj4string(sfboundary) == proj4string(sfhomes15_sp)

## [1] FALSE

Use sp function spTransform

Requires as input:

• a sp object to transform with a defined CRS

• a target CRS

Outputs a new spatial object with coordinate data in the target CRS

• It does not change the input data

Let's transform the CRS of sfboundary to be the same as that of sfhomes15_sp.

sfboundary_lonlat <- spTransform(sfboundary, CRS("+init=epsg:4326"))

Why not the other way around?

Do they match now?

How will we know?

proj4string(sfhomes15_sp) == proj4string(sfboundary_lonlat)

## [1] FALSE

plot(sfboundary_lonlat)
points(sfhomes15_sp, col="red")

Woo-hoo!

We can define the CRS of sp objects and transform them to the same CRS for mapping and spatial analysis.

Recap

# Define the CRS
proj4string(sfhomes15_sp) <- CRS("+init=epsg:4326")

#Transform the CRS
sfboundary_lonlat <- spTransform(sfboundary, CRS("+init=epsg:4326"))

Use writeOGR to save sfboundary_lonlat to a new shapefile

See ?writeOGR for help

# write transformed data to a new shapefile 
writeOGR(sfboundary_lonlat, 
          dsn = "data", 
          layer = "sfbounary_lonlat", 
          driver="ESRI Shapefile")

# is it there?
dir("data")

=

We want all data in the same CRS

Which one is best?

Geographic CRSs

• 4326 Geographic, WGS84 (default for lon/lat)

• 4269 Geographic, NAD83 (USA Fed agencies like Census)

Projected CRSs

• 5070 USA Contiguous Albers Equal Area Conic

• 3310 CA ALbers Equal Area

• 26910 UTM Zone 10, NAD83 (Northern Cal)

• 3857 Web Mercator (web maps)

See http://spatialreference.org/

Use this site to find EPSG codes and proj4 CRS strings

1. Use coordinates to convert the landmarks data frame to a SpatialPointsDataFrame
2. Use proj4string to define it's CRS as 3857 Web Mercator
3. Use spTransform to transform the landmarks data to geographic coords (WGS84)
4. Add the landmarks to the last map we created.

# Convert the DF to a SPDF
coordinates(landmarks) <-c("X","Y")
# Define the CRS with an EPSG code for Web mercator
proj4string(landmarks) <- CRS("+init=epsg:3857") 
# Transform the CRS to WGS84
landmarks_lonlat <- spTransform(landmarks, CRS("+init=epsg:4326"))
# map it
plot(sfboundary_lonlat)
points(sfhomes15_sp, col="red")
points(landmarks_lonlat, col="green")

1. Use readOGR to load the shapefile "data/sf_highways.shp"
2. Check its data type with class()
3. Check its CRS with proj4string()
4. Use spTransform if need to project it to WGS84
5. Recreate the last map and add the highways as black lines

highways <- readOGR(dsn="data", layer="sf_highways")
class(highways)
proj4string(highways)
highways_lonlat <- spTransform(highways, CRS("+init=epsg:4326"))

plot(sfboundary_lonlat)
lines(highways_lonlat, col="black")
points(sfhomes15_sp, col="red")
points(landmarks_lonlat, col="green")

## OGR data source with driver: ESRI Shapefile 
## Source: "data", layer: "sf_highways"
## with 246 features
## It has 5 fields

## [1] "SpatialLinesDataFrame"
## attr(,"package")
## [1] "sp"

## [1] "+proj=utm +zone=10 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"

# QUESTIONS?

• Geospatial Data in R
• CSV > Data Frame > ggplot/ggmap
• sp library - spatial objects and methods in R
• GDAL libary - readOGR, writeOGR
• Convert Data Frame to SPDF
• CRS definitions and transformations
• Map Overlays